Team:WHU-China/Prospect
Due to the dreadful impact of COVID-19 and extremely limited schedule, it’s a bit of frustrated that we’re unable to explore and demonstrate the whole scope of The Negotiator. However, determined to illustrate and promote this innovative prophylactic therapeutic strategy, we planned to apply for a two-phase project and strived for a proof-of-concept of The Negotiator in 2021 iGEM. Several goals were documented here for members of 2021 WHU-China to endeavour. Also, several crazy ideas about our project were brainstormed through this season, and we documented them as potential inspirations for future iGEMers.
Exploring Quenching Module by rationally engineered ancestral quorum quenching enzymes. In phase I of our project, we did a lot of work on ancestral proteins reconstitution to design engineered quorum quenching enzymes with enhanced substrate scope and catalyzing efficiency, yet the results cannot be illustrated in wet lab this year. We envision that these in silico-generated sequences will be synthesized and their functions will be tested next year, for the optimization of Quenching Module.
Testing Sensing Module in the microfluidic chips that simulate the lower respiratory tract. Despite dry lab work on inflammation, the interactions between our negotiator probiotics and immune systems remain uncertain. Before clinical experiments, we envision that an in vitro environment with full capabilities to simulate a lower respiratory tract will answer our doubts and illustrate the function of Sensing Module in a simulated in situ context.
Developing a synthetic biology start-up in Wuhan for revolutionary engineered probiotic products. Through surveys in collaborations with Tongji-China and UCAS-China, we deem that the city of Wuhan has the great potential for synthetic biology start-ups, motivated by government policies in recent years and biotechnology foundations along the history. In addition, engineered probiotics will have broad and rosy future in China, as the markets are not well explored and exploited yet.
Cell-free prototyping of signal transduction pathways as a brand-new methodology for drug screening. The bottom-up synthetic biology methods are gaining more and more attentions over the past decade, coupled with the renaissance of cell-free systems [1]. Cell-free systems were harnessed to instruct metabolic engineers to interrogate metabolism in a rapid and high-throughput pattern for pathway optimization [2], but what else research can be accelerated? Traditional in vivo methods of drug screening targeted at signal transduction pathways are not outdated but can hardly keep up with the fast pace of this omics epoch. In addition, in vivo drug screening targeted at transduction pathways is rather implicit, according to the complicated cellular machinery. Interestingly, the merits of cell-free systems, straightforward conclusion, rapid cycle and high throughput, bypass the in vivo barriers and perfectly match the omics study. Besides bacteria-lysates cell-free systems, an increasing number of liposome-based cell-free systems to simulate cells with highly controllable components are being constructed, how about reconstituting de novo cells and creating brand-new drug screening methodology? Looking forward to it.
Exploiting probiotics-based cell-free systems for accelerating the development of probiotic chassis and characterization of relevant genetic parts. Probiotics, with numerous applications to date and as promising next generation chassis, have long confused researchers with their complicated genetic engineering systems and correspondingly limited toolkits. To manipulate probiotics in genetic level, CRISPR/Cas9 methods are proposed recently [3]. However, there’s commonsense that non-model bacteria are still hard for exploitation, and their genetic parts are hard to characterize as well. Inspired by a PNAS research paper [4], we’re wondering-how about harnessing similar methods to engineer probiotics? Exploiting next generation chassis using cell-free expression systems and machine learning algorithms sounds exciting.
1. Silverman AD et al., Cell-free gene expression: an expanded repertoire of applications. Nat. Rev. Genetics, 21 (2020): 151-170.
2. Karim AS, Dudley QM et al.: In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design. Nat Chem Biol 2020.
3. Bober JR, Beisei CL, Nair NU. Synthetic biology approaches to engineer probiotics and members of the human microbiota for biomedical applications. Annual Review of Biomedical Engineering, 20 (2018): 277–300.
4. Moore SJ et al. Rapid acquisition and model-based analysis of cell-free transcription-translation reactions from nonmodel bacteria. PNAS, 115 (2018): 4340-4349.
